Processes quantitative analyses of high throughput cell migration assay. WIS-PhagoTracker facilitates morphometric analysis of modified Phagokinetic tracks that are visualized by using a screening microscope. This software applies a multi-scale segmentation algorithm to characterize several morphometric parameters such track area, perimeter, major and minor axis and solidity for each track. It can support single image files and run batch processing of multiple plates.
A computational framework to annotate complex cellular dynamics. A machine-learning method that combines state-of-the-art classification with hidden Markov modeling for annotation of the progression through morphologically distinct biological states was developed. CellCognition is published as open source software, enabling live-cell imaging-based screening with assays that directly score cellular dynamics.
Analyzes, processes and visualizes multi-dimensional microscopy images. BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes.
A free, open-source system designed for flexible, high-throughput cell image analysis. CellProfiler can address a variety of biological questions quantitatively, including standard assays (for example, cell count, size, per-cell protein levels) and complex morphological assays (for example, cell/organelle shape or subcellular patterns of DNA or protein staining).
Finds dynamic changes in pixel intensity between image frames. MUSCLEMOTION expresses the output as a relative measure of movement during muscle contraction and relaxation. It can be employed for multiparameter recording conditions and experimental settings using transmitted light microscopy, fluorescent membrane labeling, fluorescent beads embedded in soft substrates or patch clamp video recordings.
Provides a platform dedicated to the correlation of biosensor activity with the velocity of neighboring regions of the cell edge. EdgeProps is a standalone software that investigates links several parameters such as signaling activity or protrusion persistence and that includes multiple representations of edge dynamics. The application ascertains activation level and velocity at each point over time for a series of points that are equally spaced throughout the edge.
Correlates local cortical fluorescence with membrane movement. Quimp is based on the electrostatic contour migration method (ECMM) that consists of an improvement of a boundary tracking approach. It reduces sum of path lengths connecting all pairs of points, equivalent to minimizing the energy required for cell deformation. This tool is useful to study time series of several hundreds of cells per experimental condition.
A tool for segmentation, fluorescence quantification, and tracking of cells on microscopy images. CellX decodes the information across the cell membrane and guarantees optimal detection of the cell boundaries on a per-cell basis. Graph cuts account for the information of the cell boundaries through directional cross-correlations, and they automatically incorporate spatial constraints. The method accurately segments images of various cell types grown in dense cultures that are acquired with different microscopy techniques.
A user-friendly opensource software tool for tracking cells imaged with various imaging modalities, including fluorescent, phase contrast, and differential interference contrast (DIC) techniques. The main goals of the software tool are: (i) automated image quality enhancement using vignetting and alignment correction, (ii) detection and tracking of cells, (iii) editing cell paths and statistical analysis of the cell motion.
Supplies a method for ranking cellular morphodynamics. SquigglyMorph is an application permitting the investigation and the displaying of regions of protrusion and retraction. It includes features that allows users to (i) build smoothed curves (ii) assess centroid speed and persistence and (iii) display cell boundary, distribution profile of protruding boundary points, rate of area change or polarization parameter as functions of time.
Allows analysis of epithelial tissues. EpiTools automates image analysis including cell segmentation and cell tracking. It describes dynamic cellular behavior and allows users to study the power of in vivo imaging. This tool supplies a graphical user interface to simplify its utilization by users and for segmenting and tracking the contours of cell membrane signals obtained from 4D confocal imaging. It is intended primarily for biologists with no computer-science background.
Analyzes and detects cell migration and morphodynamics. ADAPT permits rapid whole-cell analysis of time-lapse videos, providing data on cell morphology, membrane velocity, and temporal changes in any fluorescent protein of interest at the cell periphery. It allows the tracking of cell migration and the automated detection of individual membrane protrusions, outputting data on local membrane velocity, change in protrusion size, and local recruitment of proteins to the cell membrane.
Investigates cellular protrusion dynamics. CellGeo is a platform dedicated to cell protrusions tracking and other changes in morphology. It is built around: (i) an unsupervised mode that allows users to manage their data and to apply default or a recorded set of parameter values and; (ii) an exploratory mode to ease settings calibration by observing their effects directly on the analysis. It also includes five modules providing features for specific protrusions identification as well as for visualization or mapping.
Allows users to submit time-lapse fluorescence image sets of focal adhesion (FA) proteins and have these images automatically analyzed. FAAS provides a set of webpages for uploading a stacked TIFF set of images for processing. The processing pipeline is then run, and the results are returned as a downloadable zip file. The user is provided with two types of visualizations that show either the entire field of view or single adhesions over time. The software can extract and quantify a wide range of properties.
Provides general purpose functionality for reading, writing, processing and analysis of images. In the context of microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and use of existing tools in the R environment for signal processing, statistical modeling, machine learning and data visualization. It uses ImageMagick to read and save images, and supports more than 80 image formats, including JPEG, TIFF, TGA, GIF and PNG. EBImage also supports standard geometric transformations such as rotation, reflection, cropping, translation and resizing. Classical image processing tools are available: linear filtering, morphological erosion and dilation, fast distance map computation, contour delineation and area filling.
A generic workflow for the study of single cell motility in high-throughput time-lapse screening data. MotIW is composed of cell tracking, cell trajectory mapping to an original feature space and hit detection according to a new statistical procedure. We show that this workflow is scalable and demonstrates its power by application to simulated data, as well as large-scale live cell imaging data. This application enables the identification of an ontology of cell motility patterns in a fully unsupervised manner.
Extracts data from fluorescently labelled cells or nuclei. NucliTrack is an easy to use and open-source package that allows users to quickly inspect and correct tracking data. Results are significantly higher throughput than if manual tracking have been realized: near 100% accuracy can be achieved, which is critical in quantifying cell fate decisions. A function permits to accommodates for batch processing of videos using the HDF5 parameter file.
Provides assistance for visualization and analysis of multi-modal, multi-process and time-lapse microscopy morphological and functional images at single-cell level. SCIP can execute an automatic or manually corrected segmentation of cells and lineages, automatic alignment of different microscopy channels and identify, measure and determine fluorescent spots. This software aims to ease the finding of relationships between cellular processes from small-scale to large-scale in single cells and cell lineages.
Segments and tracks budding yeast cells. DISCO is a comprehensive framework structured into several stages for integrated identification, segmentation and tracking of cells: (i) identification of physical features of the microfluidic device, (ii) supervised classification to identify cell centers, (iii) segmentation using a morphologically constrained cell-shape model, (iv) incorporation of temporal information to refine cell center prediction and (v) iterative greedy optimization of cell contours.
Allows users to detect, fit and predict concerted cell velocity. Bowhead is an open source program that implements a computational method using a Bayesian statistical approach. The application first detects wounds in images with labeled cells, then calculates area and perimeter of the identified wounds and lastly, from these measurements, determines the velocity. The application was developed to facilitate its incorporation into imaging pipelines for use in screening assays.
Allows to track populations of neurons with single neuron resolution in the brain of a freely moving C. elegans undergoing large motion and deformation. NeRVEclustering uses non-rigid point-set registration in order to match each segmented neuron in each volume with a set of reference volumes taken from throughout the recording. This tool primarily serves for tracking neurons in brains undergoing large deformations.
Enables cell lineage tracking. MicrobeTracker utilizes cell shape and timelapse information to achieve cell outlining. It can track fluorescently labeled molecules in cell lineages over several generations or in difficult-to-resolve samples, such as densely-packed or filamentous cells, from time-lapse sequences. This tool is delivered with an accessory tool, called SpotFinder, that detects small round spots, generating precise cell coordinates of fluorescently labeled foci inside cells.
Automates biosensor images queries. LineScan is a standalone application able to detect links between activity, distance from the edge, and velocity. The application computes edge velocity and then groups line scans according it, allowing signaling at different distances from the cell edge to be correlated with edge velocity. It can be used to clarify spatio-temporal dynamics of signaling.
An imaging system package relying on a closed-loop control algorithm to adapt the collection of a series of time-lapse images to optimize the measurement of gene expression data in individual cells. GenoSIGHT allows users to define their own functions to analyze cell properties like fluorescence, growth, shape, or intracellular distribution of proteins to any criteria defined by the user. GenoSIGHT is capable of detecting that cells are not behaving as expected and notify the operator in real-time so that the experiment can be restarted immediately.
Allows image analysis. TRACMIT permits to automate the chromatin feature extraction of mitotic cells grown on micropatterns. It allows screening of live imaging data sets for novel candidates regulating mitotic processes, such as spindle positioning. The tool can select micropatterns that contain exactly one cell, while incorporating pre-processing, tracking, data filtering and visual validation. It offers a way to monitor and quantify cell division features.
It is an organized collection of software modules for image data handling, pre-processing, segmentation, inspection and editing, post-processing, and secondary analysis. These modules can be scripted to accomplish a variety of automated image analysis tasks.
A modular, multi-platform, open-source, Java-based software delivered both as a standalone program and as a plugin for Icy. The software is designed for extracting and visualizing quantitative data from bacterial time-lapse movies. BactImAS uses a semi-automated approach where the user defines initial cells, identifies cell division events, and, if necessary, manually corrects cell segmentation with the help of user-friendly GUI and incorporated ImageJ application. The presented software simplifies quantitative analysis of time-lapse movies overall and is currently the only available software for the analysis of mycobacteria-like cells. It will be of interest to the community of both end-users and developers of time-lapse microscopy software.
A high throughput method to automatically detect the transition of a cell cluster from two to three cells in thousands of videos. livespin performs a robust implicit tracking of cells even when they are packed, overlap or are not clearly distinguishable. The approach is based on a robust fitting of two-dimensional Gaussian mixture models with two and three components on each frame of the video. livespin is composed of four steps described in this section. The first step consists in localizing the fibronectin patterns and cropping the whole video at those locations to obtain individual cluster sequences, the second step consists in fitting 2- and 3-components Gaussian mixture model (GMM) onto each frame of each video sequence and the third step consists in the identification of the first frame containing three cells (the transition from 2 cells to 3 cells) using the fitting error difference and other features computed from the GMM parameters. The final step consists in the computation of the angle of division in the identified frame.
Aims to ease the automated curation and editing of lineages of worms. AceTree is an open-source software able to handle tracked caenorhabditis elegans nuclei 4-dimensional (4D) fluorescence microscopy datasets. It provides a platform gathering a set of features for browsing, manual tracking, cell and track editing and curation of worm’s lineage data. The program is part of the StarryNite project.
A 4-D image processing platform for the work with laser scanning and wide field microscopes. TIKAL provides a registration software for correcting global movements and local deformations of cells as well as 2-D and 3-D tracking software.
A robust and fast computational procedure for tracking fluorescent markers in time-lapse microscopy. The algorithm is optimized for finding the time-trajectory of single particles in very noisy image sequences. The optimal trajectory of the particle is extracted by applying a dynamic programming optimization procedure. In addition, SpotTracker includes an optimal filter to enhance a Gaussian-like spot while attenuating the background noise.
Discovers the “classical” endpoints neuron quantification and neuronal morphology but also novel endpoints like radial migration and neuronal density distributions within the Neurosphere Assay. Omnisphero aims to automated high-content image analysis (HCA) developmental neurotoxicity (DNT) screenings. It can be applied in other 3D in vitro systems such as in the migration assay of tumor spheroids.
Provides an image analysis software for prokaryotes with complex morphologies. BacStalk is an application specialized for automated, label-free, time-resolved image analysis of stalked and non-stalked bacteria. It enables the detection of fluorescence patterns and the morphometric analysis of cell bodies, and their corresponding stalks and buds. It can also visualize fluorescence signals in cells in interactive demographs and kymographs.
A simple, user-friendly tool for interactive image classification, segmentation and analysis. It is built as a modular software framework, which currently has workflows for automated (supervised) pixel- and object-level classification, automated and semi-automated object tracking, semi-automated segmentation and object counting without detection. Most analysis operations are performed lazily, which enables targeted interactive processing of data subvolumes, followed by complete volume analysis in offline batch mode.
Restores images from microscopic data. Huygens is based on the deconvolution approach that reassigns out-of-focus light to its origin, thus improves signal-to-noise in images. It can use physically-acquired or simulated point-spread functions (PSFs) for characterization of optical system being deconvolved. The tool shows high-performance in in-house tests on deconvolution compared to other software packages. It provides intuitive wizards for parameter selection and processing.
It is the ideal "glue" for easily integrating dissimilar fluorescent microscope hardware and peripherals into a single custom workstation, while providing all the tools needed to perform meaningful analysis of acquired images. The software offers many user-friendly application modules for biology-specific analysis such as cell signaling, cell counting, and protein expression.
A free, cross-platform, open source software for high throughput time-lapse data processing for live cell imaging. TLA is a graphical tool which enables easy access to high-throughput live cell imaging for every user, regardless of the individual expertise. Beginners can easily process stacks of time-lapse data by loading an appropriate image processing setup and time-lapse evaluation setup. Advanced users can modify existing setups, or create new setups which suit their need and special experimental conditions.
Offers an ImageJ based framework which is easily extendible and has the capability to track cell lineages while being specifically designed to handle large cell displacements between frames. The methods are designed for fluorescent cells and have been used to analyse Schizosaccharomyces pombe (lower right), C2C12 mouse stem cells (upper right) or migrating RPE cells.
Provides all the tools you need to visualize, analyze and validate 3D fluorescence images from a wide range of confocal microscopy, widefield and high content screening systems and is fully integrated for a seamless user experience. Get a full picture of the biological process with rapid, interactive, high-resolution volume rendering of time resolved, multichannel 3D data sets using Volocity software.
Combines state-of-the-art automated neuron tracing and machine learning-enabled neuron classification tools. Aivia provides methods for analyzing time-lapse images. It covers a wide range of applications such as cell/nuclei counting, cell/nuclei tracking, 3D neuron detection and analysis, machine learning cell classification, particle tracking, wound healing and calcium oscillation tracking. Aivia also comes with editing tools to help get even better results.
Allows users to visualize, manipulate, and understand data from imaging modalities such as computed tomography, microscopy or Magnetic resonance imaging (MRI). Amira 3D Software for Life Sciences provides features to import and process 2D and 3D images data, visualization techniques and tools for visual analysis. Users can also create and share presentations. The base product can be customized by adding functional extensions to fit special needs in different application areas.
Contains functionalities for processing and analysis image data. GoFigure2 is a platform which allows users to visualize and navigate through 4D multichannels bio-images. Besides, it aims to provide an automatic segmentation of nuclei and cell membranes and to enable the way of extracting data from bio-images.
Manages instrument control, image processing and data analysis. SlideBook can drive hundreds of devices including microscopes, stages, lasers, wheels, piezos, scanners or shutters. It acquires data in 3D format over time, color, and specimen locations in customizable experiment protocols. This tool offers a solution to investigate images and obtain statistical data via a wide variety of algorithms while maintaining original data integrity.